The Wiki Amiga tutorial I've put is good to install SMS, but they have another tutorial about big partitions:
http://wiki.classicamiga.com/Installing_a_large_Harddrive_(4GB_or_larger)
Sorry, I don't know what happens with the link, really there is text in the page. Try google search "Installing a large Harddrive (4GB or larger)"
And remember you don't have to use the "-disableharddrivesafetycheck". If you use Windows XP no problem, and if you have Windows Vista only have to create a WinUAE shortcut on the desktop, right click on it and select "execute as administrator", to use your own HD.
I have SMS in my 32gb CF and goes right.
EDIT: (Well, disableharddrivesafetycheck is used in old WinUAE versions, but not in the latest)